Genomic and functional characterization of probiotic strains from traditional fermented dairy products in alleviating dextran sulfate sodium–induced colitis

Traditional fermented dairy products constitute a rich reservoir of probiotics and are closely associated with the maintenance of gut microbiome homeostasis and host health. However, the diversity and functional properties of probiotics in these products remain incompletely characterized. In this study, we aimed to isolate and identify novel probiotic strains from traditional fermented dairy products and systematically evaluate their probiotic attributes and mechanisms of action. Three previously uncharacterized strains-Lacticaseibacillus rhamnosus L.r1, Lacticaseibacillus rhamnosus L.r2, and Lactiplantibacillus plantarum ssp. plantarum L.p-were isolated and identified. Their probiotic features were assessed through acid and bile salt tolerance tests, survival in simulated gastrointestinal fluids, cell surface hydrophobicity, and autoaggregation capacity. Additionally, cell-free supernatants from these isolates exhibited broad-spectrum antimicrobial activity against several pathogenic bacteria. Whole-genome sequencing and comparative genomic analysis revealed the presence of an LPH homolog gene implicated in anti-inflammatory processes, along with gene clusters encoding secondary metabolites such as RiPP-like and terpene-precursor compounds. In a dextran sulfate sodium-induced murine colitis model, administration of L.r1, L.r2, or L.p significantly ameliorated colon damage, upregulated the expression of ZO-1, occludin, and IL-10, and downregulated IL-6. Fecal microbiome sequencing and functional prediction indicated that intervention with these strains restored gut microbiota balance, promoted the enrichment of beneficial genera including Akkermansia, Pediococcus, and Bacteroides, and suppressed microbial pathways related to antibiotic resistance and carbohydrate transport. These findings demonstrate that the isolated strains alleviate colitis through multifaceted mechanisms and hold strong potential as next-generation probiotics, providing both a theoretical foundation and microbial resources for developing functional foods.